I don't know about "best" but here are my favorites and the themes or aspects that indicate why:

1. A.I. Artificial Intelligence (Monica's theme)2. Star Wars: Episode II - Attack of the Clones ("Across the Stars" and "Zam the Assassin/Chase Through Coruscant")3. Star Wars: Episode V - The Empire Strikes Back ("Yoda's Theme" and "The Clash of Lightsabers")4. Indiana Jones and the Last Crusade (Grail theme)5. Star Wars: Episode I - The Phantom Menace ("Anakin's Theme" and "Duel of the Fates")6. Close Encounters of the Third Kind (The musical exchange in the final set piece)7. E.T. the Extra-Terrestrial ("The Beginning of a Friendship" and "Escape/Chase/Saying Goodbye")8. Indiana Jones and the Raiders of the Lost Ark ("The Map Room/Dawn" and "Desert Chase")9. The Terminal (Navorsky's theme)10. Harry Potter and the Prisoner of Azkaban ("A Window to the Past")

CoGro, your seemingly definitive list seems copied from a Boston Pops concert program circa 1993 with the exception of an oddly placed Saving Private Ryan. Ryan, to me, represents a Spielberg allowing Williams to not worry so much about catchy and easily hummable melodies in his music which I think represents a major step forward in the maturation and increasing interest value of their continued collaboration.

Empire, to me, is the best film score in cinema history. It's powerfully thematic (Imperial March, Yoda's Theme, Han and Leia), incredibly smart and subtle (the vocals in the approach to Cloud City reference the Siren's song, foreshadowing the impending doom facing our heroes), and tightly edited. Every note has a purpose and every track tells a story.